This subproject is one of many research subprojects utilizing the resources provided by a Center grant funded by NIH/NCRR. The subproject and investigator (PI) may have received primary funding from another NIH source, and thus could be represented in other CRISP entries. The institution listed is for the Center, which is not necessarily the institution for the investigator. In the United States, a small percentage of persons infected with the spirochete Borrelia burgdorferi (Bb) develop a chronic arthritis that is refractory to antibiotic treatment. This condition can last for months to years despite apparent eradication of the spirochete. Antibiotic treatment refractory Lyme arthritis is associated with the MHC class II alleles HLA-DR*0401 and HLA-DR*0101, which suggests that the host response to Bb is important in disease progression. The goal of this project is to determine which Bb protein-derived peptides are presented by the disease susceptibility MHC class II alleles. We have established HLA-DR*0401 and *0101 homozygous cell lines from Lyme arthritis patients for use as antigen-presenting cells in cell culture. These cells are incubated with recombinant Bb proteins or Bb whole cell sonicates. HLA-DR-peptide conjugates are immunopurified using anti-HLA-DR antibodies. Peptides are acid eluted, separated by centrifugal ultrafiltration, and purified by C18 solid-phase exraction. Purified peptides are identified by LC-MS/MS analysis followed by database searching. As a test of our methods, we have purified peptides from HLA-DR*0401 cells incubated in media alone. LC-MS/MS analysis identified numerous self-derived peptides as well as some serum-derived peptides. These results indicate that our methods are working well and we have proceeded to study Bb proteins. In our initial experiments, we expressed recombinant Bb outer surface protein A (OspA) which had been labeled with 13C6-lysine. Lysine was selected because the OspA sequence contains numerous lysine residues well distributed throughout the protein. When labeled and unlabeled OspA-MBP were mixed together and added to antigen-presenting cells, the processed peptides could be readily identified by mass spectrometry as pairs separated by intervals of exactly 6 Da. These pairs were then subjected to sequence analysis during automated LCMS data acquisition. We then progressed to the analysis of patient-derived samples and have analyzed synovial tissue from 2 controls who have arthritis but not Lyme disease and from 2 Lyme disease patients. The antigen-presented peptides are being identified using MS databases and the results for the four patients are being compared to one another to identify epitopes that may be characteristic for the Lyme patients and for the arthritis patients, and to determine whether there are allele-specific peptides. Rigorous criteria are being imposed to assure high reliability in the assignments. Some peptides have been found to bear post-translational modifications and the appropriately modified peptides are being synthesized for immunological testing. A manuscript is nearly ready to be submitted for publication in Molecular and Cellular Proteomics. Dr. Yao has been invited to give an oral presentation of the results at the 2010 ASMS meeting in Salt lake City, UT.